Background. One- or two-day intervals are generally inserted into scheduled conditioning regimens for allogeneic hematopoietic cell transplantation (HCT), primarily due to various social circumstances, such as unexpected natural adversities, abrupt deterioration of patient health, and delays in graft source arrival. We compared the clinical outcomes of patients with interrupted conditioning to those with ordinarily scheduled conditioning. Procedure. We retrospectively analyzed 83 patients (children and adolescents) with oncologic disease who underwent myeloablative conditioning with total body irradiation (TBI). Interruption of conditioning was defined as a regimen in which one or two vacant days (no chemotherapy drug administration or TBI) were added to the initially scheduled regimen. Results. Overall and event-free survival were similar between the scheduled conditioning group and the interrupted conditioning groups (P = 0.955, P = 0.908, respectively). Non-relapse mortality and relapse rates were similar between the groups (P = 0.923, P = 0.946, respectively). The engraftment rate was not affected by interruption (P = 1.000). In contrast, the incidence of grade II–IV acute graft-versus-host disease (GVHD) reached a marginally significant difference between the groups (31% vs. 11%; P = 0.083). Conditioning interruption was identified to be an independent risk factor for chronic GVHD by multivariate analysis (odds ratio: 3.72; 95% CI: 1.04–13.3; P = 0.043). Conclusion. Apart from the incidence of chronic GVHD, clinical outcomes were not affected by one- or two-day intervals during conditioning.